There was a set of recently asked questions about doing something with Internet Explorer via PowerShell. All of them contain codes to launch IE from PowerShell as an object,
I've had similar problems with COM objects that wouldn't terminate using the quit() method. Interopservices.marshall also doesn't work a lot of times. My workaround : I do a get-process to get a list of all procs before I call the com object and right after : this way I have the PID of my instance. After my script runs it kills the process using stop-process.
Not the best way to do this but at least it works